Hayabusa returned to Earth on June 13, 2010, becoming the world's first explorer to complete a round-trip voyage to an asteroid. After being released from the spacecraft, the sample return capsule landed in the Woomera Prohibited Area in the desert of South Australia. The capsule recovery team from JAXA found the capsule within 1 h of its landing. The beacon tracking system that was developed by JAXA played an important role in the tracking and discovery of the sample return capsule. The system has flexibility regarding the landing position of the capsule, because it does not rely on primary radar. In this paper, we describe the beacon tracking system and evaluate the system by discussing the results of preliminary examination and of operation on the day of re-entry.